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My answer is probably a bit late, but may still be helpful. If you forget to flush the line the air in the line will go into the peritoneal cavity. It will cause shoulder pain (between the should blades in the back) for the patient and will need to be expelled from the body in the same way gas would.
To determine if all of the fluid is drained out during CAPD you can have your patient rock slightly side to side if he/she is able to sit up. If you leave a bit of residual fluid in the peritoneal cavity it won't really hurt anything and will drain out the next time. Some patients also feel a "pinching" sensation low in their pelvis when their drain is complete.